Expand description
kbo is an approximate local aligner based on converting k-bounded matching statistics into a character representation of the underlying alignment sequence.
Currently, kbo supports three main operations:
kbo callcalls single and multi base substitutions, insertions, and deletions in a query sequence against a reference and reports their positions and sequences. Call is useful for problems that require .vcf files.kbo findmatches the k-mers in a query sequence with the reference and reports the local alignment segments found within the reference. Find is useful for problems that can be solved with blast.kbo mapmaps the query sequence against a reference sequence, and reports the nucleotide sequence of the alignment relative to the reference. Map solves the same problem as snippy and ska map.
kbo uses the Spectral Burrows-Wheeler Transform data structure that allows efficient k-mer matching between a target and a query sequence and fast retrieval of the k-bounded matching statistic for each k-mer match.
§Installing kbo
- Command line usage: see instructions at kbo-cli.
- Browser usage: try it at https://maklin.fi/kbo.
- Deploying on web: see instructions at kbo-gui.
§Usage
kbo can be run directly on fasta files without an initial indexing step.
Prebuilt indexes are supported via kbo build but are only
relevant in kbo find analyses where the reference k-mers can be
concatenated into a single contig.
kbo can read inputs compressed in the DEFLATE format (gzip, zlib, etc.). bzip2 and xz support can be enabled by adding the “bzip2” and “xz” feature flags to needletail in the kbo Cargo.toml.
§kbo call
Set up the example by downloading the fasta file for the Streptococcus pneumoniae Spn23F genome from the NCBI and the S. pneumoniae 6952_7#3 assembly from the ENA.
§Calling variants in a reference genome
In the directory with the downloaded files, run
kbo call --reference GCF_000026665.1_ASM2666v1_genomic.fna GCA_001156685.2.fasta.gz > variants.vcfThis will write the variants in the vcf v4.4 format
(click to view the first 20 lines)
##fileformat=VCFv4.4
##contig=<ID=NC_011900.1,length=2221315>
##fileDate=20250324
##source=kbo-cli v0.1.1
##reference=GCF_000026665.1_ASM2666v1_genomic.fna
##phasing=none
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
NC_011900.1 83 . G A . . . GT 1
NC_011900.1 845 . A C . . . GT 1
NC_011900.1 1064 . G A . . . GT 1
NC_011900.1 1981 . G A . . . GT 1
NC_011900.1 2392 . C T . . . GT 1
NC_011900.1 2746 . C T . . . GT 1
NC_011900.1 3236 . T C . . . GT 1
NC_011900.1 3397 . A G . . . GT 1
NC_011900.1 3993 . C T . . . GT 1
NC_011900.1 4335 . AA A . . INDEL GT 1
NC_011900.1 4504 . C A . . . GT 1
NC_011900.1 4861 . A G . . . GT 1
NC_011900.1 5007 . A T . . . GT 1§kbo find
First download the fasta sequence of the Escherichia coli Nissle 1917 genome from the NCBI and the pks island gene sequences from GitHub. Example output was generated with versions ASM71459v1 and rev 021e09f.
§Find gene sequence locations
In the directory containing the input files, run
kbo find --max-gap-len 100 --reference IHE3034_pks_island_genes.fasta GCF_000714595.1_ASM71459v1_genomic.fnaThis will produce the output (click to expand)
| query | ref | q.start | q.end | strand | length | mismatches | gap_bases | gap_opens | identity | coverage | query.contig | ref.contig |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2289596 | 2290543 | + | 948 | 0 | 0 | 0 | 100.00 | 1.90 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | IHE3034_pks_island_genes.fasta |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2239798 | 2289162 | - | 49365 | 7 | 367 | 12 | 99.24 | 98.06 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | IHE3034_pks_island_genes.fasta |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 5145962 | 5149449 | + | 3488 | 0 | 61 | 1 | 98.25 | 6.86 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | IHE3034_pks_island_genes.fasta |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 5354674 | 5356713 | + | 2040 | 1 | 0 | 0 | 99.95 | 4.08 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | IHE3034_pks_island_genes.fasta |
§Find gene sequence locations with names
If you need to know which gene in db.fasta the matches are for, add the --detailed toggle:
kbo find --detailed --reference IHE3034_pks_island_genes.fasta GCF_000714595.1_ASM71459v1_genomic.fnaThis replaces the query.contig column with the name of the contig (click to expand)
| query | ref | q.start | q.end | strand | length | mismatches | gap_bases | gap_opens | identity | coverage | query.contig | ref.contig |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2289596 | 2289808 | + | 213 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbR|locus_tag=ECOK1_RS11410|product=“colibactin biosynthesis LuxR family transcriptional regulator ClbR”|protein_id=WP_000357141.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2289809 | 2290543 | + | 735 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbA|locus_tag=ECOK1_RS11415|product=“colibactin biosynthesis phosphopantetheinyl transferase ClbA”|protein_id=WP_001217110.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2279541 | 2289162 | - | 9622 | 1 | 0 | 0 | 99.99 | 100.01 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbB|locus_tag=ECOK1_RS11405|product=“colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbB”|protein_id=WP_001518711.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2276900 | 2279500 | - | 2601 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbC|locus_tag=ECOK1_RS11400|product=“colibactin polyketide synthase ClbC”|protein_id=WP_001297908.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2276021 | 2276890 | - | 870 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbD|locus_tag=ECOK1_RS11395|product=“colibactin biosynthesis dehydrogenase ClbD”|protein_id=WP_000982270.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2275743 | 2275991 | - | 249 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbE|locus_tag=ECOK1_RS11390|product=“colibactin biosynthesis aminomalonyl-acyl carrier protein ClbE”|protein_id=WP_001297917.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2274609 | 2275739 | - | 1131 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbF|locus_tag=ECOK1_RS11385|product=“colibactin biosynthesis dehydrogenase ClbF”|protein_id=WP_000337350.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2273344 | 2274612 | - | 1269 | 1 | 0 | 0 | 99.92 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbG|locus_tag=ECOK1_RS11380|product=“colibactin biosynthesis acyltransferase ClbG”|protein_id=WP_000159201.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2268500 | 2273296 | - | 4797 | 2 | 0 | 0 | 99.96 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbH|locus_tag=ECOK1_RS11375|product=“colibactin non-ribosomal peptide synthetase ClbH”|protein_id=WP_001304254.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2265418 | 2268450 | - | 3033 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbI|locus_tag=ECOK1_RS11370|product=“colibactin polyketide synthase ClbI”|protein_id=WP_000829570.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2258874 | 2265374 | - | 6501 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbJ|locus_tag=ECOK1_RS11365|product=“colibactin non-ribosomal peptide synthetase ClbJ”|protein_id=WP_001468003.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2259498 | 2260784 | - | 1287 | 2 | 0 | 0 | 99.84 | 19.91 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbK|locus_tag=ECOK1_RS11360|product=“colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK”|protein_id=WP_000222467.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2252399 | 2258863 | - | 6465 | 2 | 0 | 0 | 99.97 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbK|locus_tag=ECOK1_RS11360|product=“colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK”|protein_id=WP_000222467.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2253845 | 2255131 | - | 1287 | 1 | 0 | 0 | 99.92 | 19.80 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbJ|locus_tag=ECOK1_RS11365|product=“colibactin non-ribosomal peptide synthetase ClbJ”|protein_id=WP_001468003.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2250943 | 2252406 | - | 1464 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbL|locus_tag=ECOK1_RS11355|product=“colibactin biosynthesis amidase ClbL”|protein_id=WP_001297937.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2249442 | 2250881 | - | 1440 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbM|locus_tag=ECOK1_RS11350|product=“precolibactin export MATE transporter ClbM”|protein_id=WP_000217768.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2245077 | 2249445 | - | 4369 | 1 | 0 | 0 | 99.98 | 100.02 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbN|locus_tag=ECOK1_RS11345|product=“colibactin non-ribosomal peptide synthetase ClbN”|protein_id=WP_001327259.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2242587 | 2245046 | - | 2460 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbO|locus_tag=ECOK1_RS11340|product=“colibactin polyketide synthase ClbO”|protein_id=WP_001029878.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2241060 | 2242574 | - | 1515 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbP|locus_tag=ECOK1_RS11335|product=“precolibactin peptidase ClbP”|protein_id=WP_002430641.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2240345 | 2241067 | - | 723 | 0 | 0 | 0 | 100.00 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbQ|locus_tag=ECOK1_RS11330|product=“colibactin biosynthesis thioesterase ClbQ”|protein_id=WP_000065646.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 2239798 | 2240310 | - | 513 | 1 | 0 | 0 | 99.81 | 100.00 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbS|locus_tag=ECOK1_RS11325|product=“colibactin self-protection protein ClbS”|protein_id=WP_000290498.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 5145962 | 5147210 | + | 1249 | 0 | 0 | 0 | 100.00 | 85.31 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbL|locus_tag=ECOK1_RS11355|product=“colibactin biosynthesis amidase ClbL”|protein_id=WP_001297937.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 5147272 | 5148479 | + | 1208 | 0 | 0 | 0 | 100.00 | 83.89 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbM|locus_tag=ECOK1_RS11350|product=“precolibactin export MATE transporter ClbM”|protein_id=WP_000217768.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 5148478 | 5149449 | + | 972 | 0 | 0 | 0 | 100.00 | 22.25 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbN|locus_tag=ECOK1_RS11345|product=“colibactin non-ribosomal peptide synthetase ClbN”|protein_id=WP_001327259.1 |
| GCF_000714595.1_ASM71459v1_genomic.fna | IHE3034_pks_island_genes.fasta | 5354674 | 5356713 | + | 2040 | 1 | 0 | 0 | 99.95 | 46.70 | NZ_CP007799.1 Escherichia coli Nissle 1917 chromosome, complete genome | clbN|locus_tag=ECOK1_RS11345|product=“colibactin non-ribosomal peptide synthetase ClbN”|protein_id=WP_001327259.1 |
Note that the current implementation --detailed slows down
the algorithm. Future versions of kbo may address this by incorporating
colors in the index structure.
§Find containment of gene sequences in assembly
Alternatively, if you are only interested in whether the contigs in
db.fasta are present in the assembly, swap the reference and query above
run
kbo find --reference GCF_000714595.1_ASM71459v1_genomic.fna IHE3034_pks_island_genes.fastawhich will return (click to expand)
| query | ref | q.start | q.end | strand | length | mismatches | gap_bases | gap_opens | identity | coverage | query.contig | ref.contig |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 513 | - | 513 | 1 | 0 | 0 | 99.81 | 0.01 | clbS|locus_tag=ECOK1_RS11325|product=“colibactin self-protection protein ClbS”|protein_id=WP_000290498.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 723 | - | 723 | 0 | 0 | 0 | 100.00 | 0.01 | clbQ|locus_tag=ECOK1_RS11330|product=“colibactin biosynthesis thioesterase ClbQ”|protein_id=WP_000065646.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 1515 | - | 1515 | 0 | 0 | 0 | 100.00 | 0.03 | clbP|locus_tag=ECOK1_RS11335|product=“precolibactin peptidase ClbP”|protein_id=WP_002430641.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 2460 | - | 2460 | 0 | 0 | 0 | 100.00 | 0.05 | clbO|locus_tag=ECOK1_RS11340|product=“colibactin polyketide synthase ClbO”|protein_id=WP_001029878.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 4368 | - | 4368 | 1 | 0 | 0 | 99.98 | 0.08 | clbN|locus_tag=ECOK1_RS11345|product=“colibactin non-ribosomal peptide synthetase ClbN”|protein_id=WP_001327259.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 1208 | + | 1208 | 0 | 0 | 0 | 100.00 | 0.02 | clbM|locus_tag=ECOK1_RS11350|product=“precolibactin export MATE transporter ClbM”|protein_id=WP_000217768.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 1440 | - | 1440 | 0 | 0 | 0 | 100.00 | 0.03 | clbM|locus_tag=ECOK1_RS11350|product=“precolibactin export MATE transporter ClbM”|protein_id=WP_000217768.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 1464 | - | 1464 | 0 | 0 | 0 | 100.00 | 0.03 | clbL|locus_tag=ECOK1_RS11355|product=“colibactin biosynthesis amidase ClbL”|protein_id=WP_001297937.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 6465 | - | 6465 | 2 | 0 | 0 | 99.97 | 0.12 | clbK|locus_tag=ECOK1_RS11360|product=“colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK”|protein_id=WP_000222467.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 6501 | - | 6501 | 0 | 0 | 0 | 100.00 | 0.12 | clbJ|locus_tag=ECOK1_RS11365|product=“colibactin non-ribosomal peptide synthetase ClbJ”|protein_id=WP_001468003.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 3033 | - | 3033 | 0 | 0 | 0 | 100.00 | 0.06 | clbI|locus_tag=ECOK1_RS11370|product=“colibactin polyketide synthase ClbI”|protein_id=WP_000829570.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 4797 | - | 4797 | 2 | 0 | 0 | 99.96 | 0.09 | clbH|locus_tag=ECOK1_RS11375|product=“colibactin non-ribosomal peptide synthetase ClbH”|protein_id=WP_001304254.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 1269 | - | 1269 | 1 | 0 | 0 | 99.92 | 0.02 | clbG|locus_tag=ECOK1_RS11380|product=“colibactin biosynthesis acyltransferase ClbG”|protein_id=WP_000159201.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 1131 | - | 1131 | 0 | 0 | 0 | 100.00 | 0.02 | clbF|locus_tag=ECOK1_RS11385|product=“colibactin biosynthesis dehydrogenase ClbF”|protein_id=WP_000337350.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 249 | - | 249 | 0 | 0 | 0 | 100.00 | 0.00 | clbE|locus_tag=ECOK1_RS11390|product=“colibactin biosynthesis aminomalonyl-acyl carrier protein ClbE”|protein_id=WP_001297917.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 870 | - | 870 | 0 | 0 | 0 | 100.00 | 0.02 | clbD|locus_tag=ECOK1_RS11395|product=“colibactin biosynthesis dehydrogenase ClbD”|protein_id=WP_000982270.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 2601 | - | 2601 | 0 | 0 | 0 | 100.00 | 0.05 | clbC|locus_tag=ECOK1_RS11400|product=“colibactin polyketide synthase ClbC”|protein_id=WP_001297908.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 9621 | - | 9621 | 1 | 0 | 0 | 99.99 | 0.18 | clbB|locus_tag=ECOK1_RS11405|product=“colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbB”|protein_id=WP_001518711.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 213 | + | 213 | 0 | 0 | 0 | 100.00 | 0.00 | clbR|locus_tag=ECOK1_RS11410|product=“colibactin biosynthesis LuxR family transcriptional regulator ClbR”|protein_id=WP_000357141.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1 | 735 | + | 735 | 0 | 0 | 0 | 100.00 | 0.01 | clbA|locus_tag=ECOK1_RS11415|product=“colibactin biosynthesis phosphopantetheinyl transferase ClbA”|protein_id=WP_001217110.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 216 | 1464 | + | 1249 | 0 | 0 | 0 | 100.00 | 0.02 | clbL|locus_tag=ECOK1_RS11355|product=“colibactin biosynthesis amidase ClbL”|protein_id=WP_001297937.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
| IHE3034_pks_island_genes.fasta | GCF_000714595.1_ASM71459v1_genomic.fna | 1156 | 4167 | + | 3012 | 1 | 0 | 0 | 99.97 | 0.06 | clbN|locus_tag=ECOK1_RS11345|product=“colibactin non-ribosomal peptide synthetase ClbN”|protein_id=WP_001327259.1 | GCF_000714595.1_ASM71459v1_genomic.fna |
§kbo map
kbo map can be used to align a query sequence against a reference sequence. This is useful in for example generating a reference-based alignment of multiple related genomes against a good reference assembly.
To run this example, download the genome sequence of the E. coli UTI89 strain from the NCBI (ASM1326v1) and E. coli Nissle 1917 (ASM71459v1).
§Reference-based alignment
Run
kbo map --reference GCF_000714595.1_ASM71459v1_genomic.fna GCF_000013265.1_ASM1326v1_genomic.fna > result.alnwhich will write the alignment sequence to result.aln.
Modules§
- derandomize
- Derandomizing noisy k-bounded matching statistics.
- format
- Converting alignment representations into various output formats.
- gap_
filling - Gap filling using matching statistics and SBWT interval lookups.
- index
- Wrapper for using the sbwt API to build and query SBWT indexes.
- translate
- Translating deterministic k-bounded matching statistics into alignments.
- variant_
calling - Call all variants between a query and a reference.
Structs§
- Build
Opts - Options and parameters for SBWT construction.
- Call
Opts - Options and parameters for call
- Find
Opts - Options and parameters for find
- MapOpts
- Options and parameters for map
- Match
Opts - Options and parameters for matches
Functions§
- build
- Builds an SBWT index from some fasta or fastq files.
- call
- Calls variants between a query and a reference sequence.
- find
- Finds the k-mers from an SBWT index in a query fasta or fastq file.
- map
- Maps a query sequence against a reference sequence.
- matches
- Matches a query fasta or fastq file against an SBWT index.